Example usage for org.apache.shiro SecurityUtils getSubject

List of usage examples for org.apache.shiro SecurityUtils getSubject

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Introduction

In this page you can find the example usage for org.apache.shiro SecurityUtils getSubject.

Prototype

public static Subject getSubject()

Source Link

Document

Returns the currently accessible Subject available to the calling code depending on runtime environment.

Usage

From source file:au.org.theark.lims.web.component.subjectlims.subject.SubjectContainerPanel.java

License:Open Source License

protected WebMarkupContainer initialiseSearchResults() {
    searchResultListPanel = new SearchResultListPanel("searchResults", arkContextMarkup, containerForm,
            arkCrudContainerVO, studyNameMarkup, studyLogoMarkup, treeModel);

    subjectProvider = new ArkDataProvider2<LimsVO, LinkSubjectStudy>() {

        private static final long serialVersionUID = 1L;

        public int size() {

            // Restrict search if Study selected in Search form
            List<Study> studyList = new ArrayList<Study>(0);

            Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
                    .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
            if (sessionStudyId != null) {
                Study study = iArkCommonService.getStudy(sessionStudyId);

                if (criteriaModel.getObject().getStudy() != null
                        && criteriaModel.getObject().getStudy().getId() != null) {
                    // Restrict search to study in drop-down
                    studyList.add(criteriaModel.getObject().getStudy());
                } else {
                    if (study.getParentStudy() != null && study.getParentStudy().equals(study)) {
                        studyList = criteriaModel.getObject().getStudyList();
                        if (studyList.isEmpty()) {
                            studyList = containerForm.getStudyListForUser();
                        }/* w  ww . j  a  v a  2 s .c  o m*/
                    } else {
                        studyList.add(study);
                    }
                }
            }

            return iLimsSubjectService.getSubjectCount(criteriaModel.getObject(), studyList);
        }

        public Iterator<LinkSubjectStudy> iterator(int first, int count) {
            List<LinkSubjectStudy> listSubjects = new ArrayList<LinkSubjectStudy>(0);

            // Restrict search if Study selected in Search form
            List<Study> studyList = new ArrayList<Study>(0);

            Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
                    .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
            if (sessionStudyId != null) {
                Study study = iArkCommonService.getStudy(sessionStudyId);

                if (criteriaModel.getObject().getStudy() != null
                        && criteriaModel.getObject().getStudy().getId() != null) {
                    // Restrict search to study in drop-down
                    studyList.add(criteriaModel.getObject().getStudy());
                } else {
                    if (study.getParentStudy() != null && study.getParentStudy().equals(study)) {
                        studyList = criteriaModel.getObject().getStudyList();
                        if (studyList.isEmpty()) {
                            studyList = containerForm.getStudyListForUser();
                        }
                    } else {
                        studyList.add(study);
                    }
                }
            }

            listSubjects = iLimsSubjectService.searchPageableSubjects(criteriaModel.getObject(), studyList,
                    first, count);
            return listSubjects.iterator();
        }
    };
    subjectProvider.setCriteriaModel(this.cpModel);

    dataView = searchResultListPanel.buildDataView(subjectProvider);
    dataView.setItemsPerPage(iArkCommonService.getRowsPerPage());

    AjaxPagingNavigator pageNavigator = new AjaxPagingNavigator("navigator", dataView) {

        private static final long serialVersionUID = 1L;

        @Override
        protected void onAjaxEvent(AjaxRequestTarget target) {
            target.add(arkCrudContainerVO.getSearchResultPanelContainer());
        }
    };
    searchResultListPanel.add(pageNavigator);
    searchResultListPanel.add(dataView);
    arkCrudContainerVO.getSearchResultPanelContainer().add(searchResultListPanel);
    return arkCrudContainerVO.getSearchResultPanelContainer();
}

From source file:au.org.theark.phenotypic.job.PhenoDataUploadExecutor.java

License:Open Source License

public void run() throws Exception {

    SchedulerFactory sf = new StdSchedulerFactory();
    Scheduler sched = sf.getScheduler();
    Log.warn("executor " + uidsToUpload.size());
    JobDetail phenoDataUploadJob = newJob(PhenoDataUploadJob.class).withIdentity("PhenoDataUploadJob", "group2")
            .build();// www.j  av  a2  s  .  c o  m
    // pass initialization parameters into the job
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.IARKCOMMONSERVICE, iArkCommonService);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.IPHENOSERVICE, iPhenoService);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.UPLOADID, uploadId);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.STUDY_ID, studyId);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.REPORT, report);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.FILE_FORMAT, fileFormat);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.INPUT_STREAM, inputStream);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.DELIMITER, delimiter);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.SIZE, size);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.LIST_OF_UIDS_TO_UPDATE, uidsToUpload);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.PHENO_COLLECTION, phenoCollection);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.PHENO_FIELD_GROUP, phenoDataSetGroup);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.OVERWRITE_EXISTING, overwriteExisting);
    phenoDataUploadJob.getJobDataMap().put(PhenoDataUploadJob.USERNAME,
            SecurityUtils.getSubject().getPrincipal().toString());
    Date startTime = nextGivenSecondDate(null, 1);
    SimpleTrigger trigger1 = newTrigger().withIdentity("PhenoDataUploadJobTrigger", "group1").startAt(startTime)
            .withSchedule(simpleSchedule()).build();
    sched.scheduleJob(phenoDataUploadJob, trigger1);
    //      log.warn(studyUploadJob.getKey() + " will run at: " + scheduleTime1 + " and repeat: " + trigger1.getRepeatCount() + " times, every " + trigger1.getRepeatInterval() / 1000 + " seconds");
    // All of the jobs have been added to the scheduler, but none of the jobs will run until the scheduler has been started
    sched.start();
    //sched.triggerJob(phenoDataUploadJob.getKey());
}

From source file:au.org.theark.phenotypic.model.dao.PhenotypicDao.java

License:Open Source License

public void createAuditHistory(AuditHistory auditHistory, String userId, Study study) {
    Date date = new Date(System.currentTimeMillis());

    if (userId == null) {// if not forcing a userID manually, get
        // currentuser
        Subject currentUser = SecurityUtils.getSubject();
        auditHistory.setArkUserId((String) currentUser.getPrincipal());
    } else {/*from  w  w w .j  a va  2 s. com*/
        auditHistory.setArkUserId(userId);
    }
    if (study == null) {
        Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
        if (sessionStudyId != null && auditHistory.getStudyStatus() == null) {
            auditHistory.setStudyStatus(getStudy(sessionStudyId).getStudyStatus());
        } else {

            if (auditHistory.getEntityType().equalsIgnoreCase(au.org.theark.core.Constants.ENTITY_TYPE_STUDY)) {
                Study studyFromDB = getStudy(auditHistory.getEntityId());
                if (studyFromDB != null) {
                    auditHistory.setStudyStatus(studyFromDB.getStudyStatus());
                }
            }
        }
    } else {
        auditHistory.setStudyStatus(study.getStudyStatus());
    }
    auditHistory.setDateTime(date);
    getSession().save(auditHistory);
}

From source file:au.org.theark.phenotypic.util.PhenoDataSetFieldImporter.java

License:Open Source License

/**
 * PhenotypicImport constructor/*from   w ww  .  j  av  a  2 s  .c  o  m*/
 * 
 * @param studyId
 *           study identifier in context
 * @param arkFunction
 *           the function that this CustomField import should attach to
 * @param iArkCommonService
 *           the common service for dao
 * @param fileFormat
 *           format of the file uploaded
 * @param delimiterChar
 *           delimiter of the file data (comma, tab etc)
 */
public PhenoDataSetFieldImporter(Study study, ArkFunction arkFunction,
        IArkCommonService<Void> iArkCommonService, IPhenotypicService iPhenotypicService, String fileFormat,
        char delimiterChar) {
    this.study = study;
    this.iArkCommonService = iArkCommonService;
    this.iPhenotypicService = iPhenotypicService;
    this.fileFormat = fileFormat;
    this.phenotypicDelimChr = delimiterChar;
    this.arkFunction = arkFunction;
    Long sessionModuleId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.ARK_MODULE_KEY);
    this.arkModule = iArkCommonService.getArkModuleById(sessionModuleId);
}

From source file:au.org.theark.phenotypic.util.PhenoDataSetFieldImportValidator.java

License:Open Source License

/**
 * CustomFieldImportValidator constructor
 * @param iArkCommonService/* w w w  . j a  v a  2s. c o m*/
 * @param uploadVo
 */
public PhenoDataSetFieldImportValidator(IArkCommonService<Void> iArkCommonService,
        IPhenotypicService iPhenotypicService, UploadVO uploadVo) {
    this.iArkCommonService = iArkCommonService;
    this.iPhenotypicService = iPhenotypicService;
    this.arkFunction = uploadVo.getUpload().getArkFunction();

    // Set study in context
    Long studyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    if (studyId != null) {
        Study study = iArkCommonService.getStudy(studyId);
        this.study = study;
    }

    this.fileValidationMessages = new ArrayList<String>();
    this.dataValidationMessages = new ArrayList<String>();

    String filename = uploadVo.getFileUpload().getClientFileName();
    this.fileFormat = filename.substring(filename.lastIndexOf('.') + 1).toUpperCase();

    this.delimChr = uploadVo.getUpload().getDelimiterType().getDelimiterCharacter();

}

From source file:au.org.theark.phenotypic.util.PhenoDataUploadValidator.java

License:Open Source License

public PhenoDataUploadValidator() {
    super();//from   ww w .  j av a 2s.  c  om
    Subject currentUser = SecurityUtils.getSubject();
    studyId = (Long) currentUser.getSession().getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    this.study = iArkCommonService.getStudy(studyId);
    this.existantSubjectUIDRows = new HashSet<Integer>();
    this.nonExistantUIDs = new HashSet<Integer>();
    this.errorCells = new HashSet<ArkGridCell>();
    this.warningRows = new HashSet<Integer>();
    this.insertCells = new HashSet<ArkGridCell>();
    simpleDateFormat.setLenient(false);
}

From source file:au.org.theark.phenotypic.util.PhenoDataUploadValidator.java

License:Open Source License

@SuppressWarnings("unchecked")
public PhenoDataUploadValidator(IArkCommonService iArkCommonService, IPhenotypicService iPhenotypicService) {
    super();/*from  w  w  w.j a  v  a  2 s.co  m*/
    this.iArkCommonService = iArkCommonService;
    this.iPhenotypicService = iPhenotypicService;
    Subject currentUser = SecurityUtils.getSubject();
    studyId = (Long) currentUser.getSession().getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    this.study = iArkCommonService.getStudy(studyId);
    this.existantSubjectUIDRows = new HashSet<Integer>();
    this.nonExistantUIDs = new HashSet<Integer>();
    this.errorCells = new HashSet<ArkGridCell>();
    this.warningRows = new HashSet<Integer>();
    this.insertCells = new HashSet<ArkGridCell>();
    simpleDateFormat.setLenient(false);
}

From source file:au.org.theark.phenotypic.web.component.phenodatacategory.form.SearchForm.java

License:Open Source License

/**
 * @param id//w  ww. j  a  v  a2s.  com
 */
public SearchForm(String id, CompoundPropertyModel<PhenoDataSetCategoryVO> cpModel, FeedbackPanel feedBackPanel,
        ArkCrudContainerVO arkCrudContainerVO) {

    super(id, cpModel, feedBackPanel, arkCrudContainerVO);
    this.cpModel = cpModel;
    this.feedbackPanel = feedBackPanel;
    this.arkCrudContainerVO = arkCrudContainerVO;
    initialiseFieldForm();
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    disableSearchForm(sessionStudyId, "There is no study in context. Please select a study");
}

From source file:au.org.theark.phenotypic.web.component.phenodatacategory.form.SearchForm.java

License:Open Source License

/**
 * Get custom field category collection from model.
 * @return//from  www .java2  s.c o  m
 */
/*private Collection<PhenoDataSetCategory> getParentCategoryCollectionFromModel(){
   PhenoDataSetCategory phenoDataSetCategory=cpModel.getObject().getPhenoDataSetCategory(); 
   Study study=phenoDataSetCategory.getStudy();
   ArkFunction arkFunction=phenoDataSetCategory.getArkFunction();
   try {
 //phenoDataSetCategoryCollection = iPhenotypicService.getPhenoParentCategoryList(study, arkFunction);
   } catch (ArkSystemException e) {
 // TODO Auto-generated catch block
 e.printStackTrace();
   }
   return phenoDataSetCategoryCollection;
}*/

@Override
protected void onSearch(AjaxRequestTarget target) {
    target.add(feedbackPanel);
    final Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    // Get a list of all Fields for the Study in context
    Study study = iArkCommonService.getStudy(sessionStudyId);
    getModelObject().getPhenoDataSetCategory().setStudy(study);

    long count = iPhenotypicService.getPhenoDataSetCategoryCount(getModelObject().getPhenoDataSetCategory());
    if (count <= 0L) {
        this.info("No records match the specified criteria.");
        target.add(feedbackPanel);
    }

    arkCrudContainerVO.getSearchResultPanelContainer().setVisible(true);// Make the WebMarkupContainer that houses the search results visible
    target.add(arkCrudContainerVO.getSearchResultPanelContainer());
}

From source file:au.org.theark.phenotypic.web.component.phenodatacategory.PhenoDataCategoryContainerPanel.java

License:Open Source License

protected void prerenderContextCheck() {
    // Get the Study and Module out of context
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    Long sessionModuleId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.ARK_MODULE_KEY);

    if ((sessionStudyId != null) && (sessionModuleId != null)) {
        Study study = null;/*ww  w. jav a2s. c o m*/
        study = iArkCommonService.getStudy(sessionStudyId);
        ArkModule arkModule = iArkCommonService.getArkModuleById(sessionModuleId);

        if (study != null && arkModule != null) {
            cpModel.getObject().getPhenoDataSetCategory().setStudy(study);
            // TODO: Maybe check that the primary function supplied is of the same module?
        }
    }
}